If the stop state of a fuel cell system continues for long in a low temperature environment such as outdoors in cold regions, there is a danger that moisture within the system will freeze. Such freezing may cause breakdown, so many methods have been developed and proposed to prevent freezing in fuel cell systems to date. For example, in Japanese Patent Application Laid-open No. 2003-151601, a method of preventing freezing is disclosed in which when stopping a fuel cell, the fuel cell is controlled to stop after the temperature of the fuel cell has been raised, to extend the time before freezing occurs in the fuel cell in the stop state, thereby preventing the temperature of the fuel cell from dropping to a temperature to cause freezing when the fuel cell is restarted.